Merge remote-tracking branch 'upstream/master' into gptmdApproachUpdate

smith-chem-wisc · Sep 19, 2024 · 22fb336 · 22fb336
2 parents 7a7dad6 + 4d5e0ef
commit 22fb336
Show file tree

Hide file tree

Showing 10 changed files with 44 additions and 12 deletions.
diff --git a/MetaMorpheus/CMD/CMD.csproj b/MetaMorpheus/CMD/CMD.csproj
@@ -24,7 +24,7 @@
     <PackageReference Include="Microsoft.ML.CpuMath" Version="3.0.1" />
     <PackageReference Include="Microsoft.ML.FastTree" Version="3.0.1" />
     <PackageReference Include="Microsoft.NETCore.App" Version="2.2.8" />
-    <PackageReference Include="mzLib" Version="1.0.551" />
+    <PackageReference Include="mzLib" Version="1.0.552" />
     <PackageReference Include="Nett" Version="0.15.0" />
   </ItemGroup>
 

diff --git a/MetaMorpheus/EngineLayer/EngineLayer.csproj b/MetaMorpheus/EngineLayer/EngineLayer.csproj
@@ -21,7 +21,7 @@
     <PackageReference Include="Microsoft.ML.CpuMath" Version="3.0.1" />
     <PackageReference Include="Microsoft.ML.FastTree" Version="3.0.1" />
     <PackageReference Include="Microsoft.NETCore.App" Version="2.2.8" />
-    <PackageReference Include="mzLib" Version="1.0.551" />
+    <PackageReference Include="mzLib" Version="1.0.552" />
     <PackageReference Include="NETStandard.Library" Version="2.0.3" />
     <PackageReference Include="Nett" Version="0.15.0" />
     <PackageReference Include="Newtonsoft.Json" Version="13.0.3" />

diff --git a/MetaMorpheus/EngineLayer/FdrAnalysis/FdrInfo.cs b/MetaMorpheus/EngineLayer/FdrAnalysis/FdrInfo.cs
@@ -10,5 +10,16 @@ public class FdrInfo
         public double QValueNotch { get; set; }
         public double PEP { get; set; }
         public double PEP_QValue { get; set; }
+
+        /// <summary>
+        /// Creates a new FdrInfo object where Q-Values and PEP_Qvalues are set to 2 by default
+        /// This is done to avoid situations where q-values aren't calcualted for a given peptides, but it is still
+        /// reported in the final results. 
+        /// </summary>
+        public FdrInfo()
+        {
+            QValue = 2;
+            PEP_QValue = 2;
+        }
     }
 }
diff --git a/MetaMorpheus/EngineLayer/FdrAnalysis/PEPAnalysisEngine.cs b/MetaMorpheus/EngineLayer/FdrAnalysis/PEPAnalysisEngine.cs
@@ -22,6 +22,27 @@ namespace EngineLayer
 {
     public class PepAnalysisEngine
     {
+        private int _randomSeed = 42;
+
+        /// <summary>
+        /// This method contains the hyper-parameters that will be used when training the machine learning model
+        /// </summary>
+        /// <returns> Options object to be passed in to the FastTree constructor </returns>
+        public Microsoft.ML.Trainers.FastTree.FastTreeBinaryTrainer.Options BGDTreeOptions =>
+            new Microsoft.ML.Trainers.FastTree.FastTreeBinaryTrainer.Options
+            {
+                NumberOfThreads = 1,
+                NumberOfTrees = 400,
+                MinimumExampleCountPerLeaf = 10,
+                NumberOfLeaves = 20,
+                LearningRate = 0.2,
+                LabelColumnName = "Label",
+                FeatureColumnName = "Features",
+                Seed = _randomSeed,
+                FeatureSelectionSeed = _randomSeed,
+                RandomStart = false
+            };
+
         private static readonly double AbsoluteProbabilityThatDistinguishesPeptides = 0.05;
 
         //These two dictionaries contain the average and standard deviations of hydrophobicitys measured in 1 minute increments accross each raw
@@ -105,10 +126,10 @@ public string ComputePEPValuesForAllPSMs()
                 }
             }
 
-            MLContext mlContext = new MLContext();
+            MLContext mlContext = new MLContext(seed: _randomSeed);
             TransformerChain<BinaryPredictionTransformer<Microsoft.ML.Calibrators.CalibratedModelParametersBase<Microsoft.ML.Trainers.FastTree.FastTreeBinaryModelParameters, Microsoft.ML.Calibrators.PlattCalibrator>>>[] trainedModels = new TransformerChain<BinaryPredictionTransformer<Microsoft.ML.Calibrators.CalibratedModelParametersBase<Microsoft.ML.Trainers.FastTree.FastTreeBinaryModelParameters, Microsoft.ML.Calibrators.PlattCalibrator>>>[numGroups];
 
-            var trainer = mlContext.BinaryClassification.Trainers.FastTree(labelColumnName: "Label", featureColumnName: "Features", numberOfTrees: 400);
+            var trainer = mlContext.BinaryClassification.Trainers.FastTree(BGDTreeOptions);
             var pipeline = mlContext.Transforms.Concatenate("Features", TrainingVariables)
                 .Append(trainer);
 

diff --git a/MetaMorpheus/GUI/GUI.csproj b/MetaMorpheus/GUI/GUI.csproj
@@ -55,7 +55,7 @@
     <PackageReference Include="Microsoft.ML.CpuMath" Version="3.0.1" />
     <PackageReference Include="Microsoft.ML.FastTree" Version="3.0.1" />
     <PackageReference Include="Microsoft.NETCore.App" Version="2.2.8" />
-    <PackageReference Include="mzLib" Version="1.0.551" />
+    <PackageReference Include="mzLib" Version="1.0.552" />
     <PackageReference Include="Nett" Version="0.15.0" />
     <PackageReference Include="Newtonsoft.Json" Version="13.0.3" />
     <PackageReference Include="OxyPlot.Core" Version="2.0.0" />

diff --git a/MetaMorpheus/GuiFunctions/GuiFunctions.csproj b/MetaMorpheus/GuiFunctions/GuiFunctions.csproj
@@ -16,7 +16,7 @@
   <ItemGroup>
     <PackageReference Include="itext7" Version="8.0.5" />
     <PackageReference Include="itext7.bouncy-castle-adapter" Version="8.0.5" />
-    <PackageReference Include="mzLib" Version="1.0.551" />
+    <PackageReference Include="mzLib" Version="1.0.552" />
     <PackageReference Include="OxyPlot.Wpf" Version="2.0.0" />
     <PackageReference Include="Svg" Version="3.4.7" />
   </ItemGroup>

diff --git a/MetaMorpheus/TaskLayer/SearchTask/PostSearchAnalysisTask.cs b/MetaMorpheus/TaskLayer/SearchTask/PostSearchAnalysisTask.cs
@@ -137,8 +137,8 @@ private void CalculatePsmAndPeptideFdr(List<SpectralMatch> psms, string analysis
             // this could cause weird PSM FDR issues
 
             Status("Estimating PSM FDR...", Parameters.SearchTaskId);
-            new FdrAnalysisEngine(psms, Parameters.NumNotches, CommonParameters, this.FileSpecificParameters, 
-                new List<string> { Parameters.SearchTaskId }, analysisType: analysisType, doPEP: doPep, outputFolder: Parameters.OutputFolder).Run();
+            new FdrAnalysisEngine(psms, Parameters.NumNotches, CommonParameters, this.FileSpecificParameters,
+                    new List<string> { Parameters.SearchTaskId }, analysisType: analysisType, doPEP: doPep, outputFolder: Parameters.OutputFolder).Run();
 
             Status("Done estimating PSM FDR!", Parameters.SearchTaskId);
         }

diff --git a/MetaMorpheus/TaskLayer/TaskLayer.csproj b/MetaMorpheus/TaskLayer/TaskLayer.csproj
@@ -21,7 +21,7 @@
     <PackageReference Include="Microsoft.ML.CpuMath" Version="3.0.1" />
     <PackageReference Include="Microsoft.ML.FastTree" Version="3.0.1" />
     <PackageReference Include="Microsoft.NETCore.App" Version="2.2.8" />
-    <PackageReference Include="mzLib" Version="1.0.551" />
+    <PackageReference Include="mzLib" Version="1.0.552" />
     <PackageReference Include="NetSerializer" Version="4.1.2" />
     <PackageReference Include="Nett" Version="0.15.0" />
   </ItemGroup>

diff --git a/MetaMorpheus/Test/Test.csproj b/MetaMorpheus/Test/Test.csproj
@@ -24,7 +24,7 @@
     <PackageReference Include="Microsoft.ML" Version="3.0.1" />
     <PackageReference Include="Microsoft.ML.CpuMath" Version="3.0.1" />
     <PackageReference Include="Microsoft.ML.FastTree" Version="3.0.1" />
-    <PackageReference Include="mzLib" Version="1.0.551" />
+    <PackageReference Include="mzLib" Version="1.0.552" />
     <PackageReference Include="NUnit" Version="4.1.0" />
     <PackageReference Include="NUnit3TestAdapter" Version="4.6.0" />
     <PackageReference Include="Microsoft.NET.Test.Sdk" Version="17.10.0" />

diff --git a/MetaMorpheus/Test/XLTest.cs b/MetaMorpheus/Test/XLTest.cs
@@ -561,8 +561,8 @@ public static void XlTest_MoreComprehensive()
                 }
             }
 
-            Assert.AreEqual(47, inter);
-            Assert.AreEqual(73, intra);
+            Assert.AreEqual(53, inter);
+            Assert.AreEqual(81, intra);
             Assert.AreEqual(0, unnasignedCrossType);